They spoke about omentum, chemosynthesis, chromothripsis, and… Tasmanian devils? This year’s virtual two-day SMRT Leiden Scientific Symposium and Informatics Developers Meeting was certainly educational. With the pandemic and increased difficulty in being able to connect in person, we wanted to provide a forum for young investigators, post docs, and faculty to come together and share their research experiences during these abnormal times. The result? 27 speakers—the majority of whom were young investigators—sharing data and discoveries, and their advice for early-career scientists. There was a great spectrum of presentations. The first keynote featured fun facts about Dominette (first Bos taurus…
Hibernating bears have heart rates of 10-15 beats per minute, yet they do not develop congestive heart failure. Despite accumulating enormous amounts of fat and acquiring insulin resistance, they do not suffer metabolic diseases. And they maintain muscle strength in the near absence of weight-bearing activity.Iso-Seq study has revealed differential tissue-specific isoform changes in brown bears If we could crack these feats of physiology, perhaps we could apply the knowledge towards therapeutic targets for the prevention and treatment of numerous human diseases. The Project that Shed Light on the Metabolic Mystery of Brown Bears Washington State University researchers have…
Today we’re pleased to announce the launch of a new HiFi Sequencing workflow along with a software update for the Sequel II and Sequel IIe Systems that will increase the number of HiFi reads at or above 99.9% accuracy (QV30) for whole genome sequencing-based applications. Together, these advances will improve the quality of HiFi Sequencing while providing an efficient and scalable workflow for sequencing hundreds to thousands of whole human genomes per year on Sequel Systems. This high-throughput sequencing and analysis workflow release includes a new HiFi library prep protocol offering a three-fold reduction in DNA input, enabling HiFi sequencing with limited sample quantities (neonatal…
Today we’re pleased to announce the three winners of our latest SMRT Grant which called for teams of researchers and collaborative projects that could be addressed using the power of HiFi sequencing. The winners are seeking to solve a diverse set of questions from mussel-hopping transmissible cancer to the power of pistachios to help tackle climate change, and sex determination in bearded dragons. The 2020 HiFi for All – Collaborations SMRT Grant Program was open to scientists worldwide and offered three winning projects awards of up to 10 SMRT Cells 8M and sequencing on the Sequel II or…
Sequoia sempervirens is one of the tallest living trees on Earth, often reaching up to 300 ft It’s been a year since we took a little field trip to Stanford to collect samples from the giant California redwood (Sequoia sempervirens) with the goal of assembling its ginormous 27 Gb genome. What would have been considered a herculean effort not that many years ago was accomplished in only a few weeks by a handful of personnel —Emily Hatas (@EmilyHatas), Greg Young (@PacbioGreg), Michelle Vierra (@the_mvierra), and Greg Concepcion (@phototrophic) — in their spare time. As detailed in this blog post, the…
UPDATE — September 3, 2021: This paper is now published in Genome Biology. ORIGINAL POST A team of scientists from KAUST used a new rapid de novo assembly workflow to create genomes of the Eucalyptus species E. camaldulensis What does the ideal genome assembly look like? High-quality, free of errors, with no gaps, and all haplotypes resolved. It’s a big ask, especially with challenging genomes like plants that are rich in repetitive content with high levels of heterozygosity and complex polyploidy. Moreover, such assemblies often require a combination of technologies, such as sequencing plus optical mapping. But a team…
A high resolution reference genome for the rhesus macaque could help us better understand human disease. They may not be as well known as our chimpanzee or gorilla cousins, but macaques have played many key roles in scientific progress over the last half century. From launching into orbit during the early days of space travel to revealing the genetics of neurodevelopmental disorders and infectious diseases today, the rhesus macaque remains a key research primate around the world. A new, comprehensively annotated reference genome unveiled last month boosts the potential of the most widely used non-human primate in biomedical research even…
The SMRTbell gDNA Sample Amplification Kit enables whole genome amplification starting from as little as 5 ng of genomic DNA. It’s one of the questions we hear most often from scientists working with small organisms: Is it possible to generate truly high-quality, long-read data from minuscule amounts of DNA? With our new kit for ultra-low DNA input projects, the answer is: Absolutely! The new workflow dramatically reduces the requirements for DNA quantity. Now, scientists need only 5 ng of genomic DNA to kick off a SMRT Sequencing project — that’s less than 2% of the starting volume needed for our…
With PacBio HiFi sequencing data now readily available for organisms of any size, many exciting results have been published featuring new de novo assembly methods optimized for highly accurate long reads. These methods have produced assemblies for a variety of organisms at quality levels never before thought possible — as measured by completeness, contiguity and correctness. We feel privileged to collaborate with the scientific community on the development of these tools. From Small to Tall When the USDA wanted to rapidly assemble the Asian Giant Hornet as part of its real-time invasive species response initiative, they turned to a tool…
A pangenome identifies which portions of the genome are unique and which overlap and are therefore core to the species. It has recently become apparent how important it is to sequence more than one individual to characterize the genomic variation within a species. This makes sense if you consider that sexually reproducing organisms are a mix of their parents and, therefore, not identical. This is just as true in crops as it is in humans. So, it’s not surprising that when a group of researchers from several institutions in China embarked on de novo genome assemblies of several accessions of…
How do bacteria manipulate plant biology to cause blight and rot? Why are some pathogen strains more virulent than others? How can we engineer resistant staple food crops? These are pressing questions facing researchers looking to sustain and increase crop production against the backdrop of a changing environment. For one major clade of pathogens, Xanthomonas spp, the answers lay locked within TAL effector genes (TALEs), but assembling these highly variable, repetitive regions was a long-standing obstacle. The key to finally unraveling the tangled assemblies was PacBio long-read sequencing. Code-breaker Adam J. Bogdanove from Cornell University. Photo by Jesse Winter Plant…
With a nickname like “murder hornet,” it’s no wonder the two-inch long Asian giant hornet (Vespa mandarinia) has caused a stir amongst those terrified of insect invasions. Various species of paper wasp (left) compared to the Asian giant hornet (right) Photo by Hanna Royals, USDA. The wasps — which are actually more dangerous to bees than humans — have made another recent appearance in Washington state, and Agricultural Research Service (ARS) scientists are hoping a new rapidly-generated genome sequence of one of the insects will help in their quest to quash an invasion. Released August 6, the first high-quality genome…
Tackling larger and larger genomes has been an attractive pursuit for many scientists as sequencing technologies improve at rapid rates. But what about the other end of the spectrum — the tiny organisms that comprise much of the diversity of life? An obvious obstacle to decoding the DNA of small organisms such as insects, nematodes and other arthropods is collecting enough of it to actually sequence (usually multiple micrograms worth). Until recently, the solution was to pool DNA from many of these tiny creatures to create a representative sample, and extrapolate the biology of the individual constituents from there. But…
The new and updated species in Ensembl 99 from the Vertebrate Genomes Project (VGP) Meerkats, yaks, geese, and lots of flies — oh my! A full menagerie of new and updated animal genomes has been released by the Ensembl project. The Ensembl 99 release includes a variety of vertebrates, plants, mosquitos, and flies, as well as updates of human gene annotation and variation data. Among them are 38 new species and two dog breeds (Great Dane and Basenji), as well as four updated genome assemblies. Many were created using PacBio sequencing data. Thirteen of the new assemblies have…
Matt Hufford, associate professor at Iowa State University, helped produce a 26-line maize pangenome assembly collection Maize researchers have been rejoicing over a New Year’s gift delivered by a group of 33 scientists: A 26-line “pangenome” reference collection. The multi-institutional consortium of researchers used the Sequel System and BioNano Genomics optical mapping to create the assemblies and high-confidence annotations. They released the results on January 9, and in several presentations at the Plant and Animal Genome XXVIII Conference, less than two years after the ambitious project was funded by a $2.8 million National Science Foundation grant. The collection includes comprehensive,…